2NOZ | PD0897 - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURE OF Q315F HUMAN 8-OXOGUANINE GLYCOSYLASE DISTAL CROSSLINK TO 8-OXOGUANINE DNA

Authors :   C. T. Radom, A. Banerjee, G. L. Verdine

Date :   26 Oct 06 (Deposition) - 21 Nov 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.43

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   N-Glycosylase/Dna Lyase, Dna Repair, 8-Oxoguanine, Hydrolase, Lyase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. T. Radom, A. Banerjee, G. L. Verdine
Structural Characterization Of Human 8-Oxoguanine Dna Glycosylase Variants Bearing Active Site Mutations.
J. Biol. Chem. V. 282 9182 2007
PubMed-ID: 17114185 | Reference-DOI: 10.1074/JBC.M608989200
(for further references see the PDB file header)

*Molecule 1 - 5'- D(GPGTPAPGPAPCPCPTPGPGPAPCPGPC)-3'**
	Chains	:	B
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 2 - 5'-D(GCPGPTPCPCPAP(G42) PGPTPCPTPAPCPC)-3'**
	Chains	:	C
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - N-GLYCOSYLASE/DNA LYASE
	Chains	:	A
	EC Number	:	3.2.2.-, 4.2.99.18
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET30A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	8-OXOGUANINE DNA GLYCOSYLASE, DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE
	Gene	:	OGG1, MMH, MUTM, OGH1
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	AP LYASE

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	8OG	1	Mod. Nucleotide	8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
2	CA	2	Ligand/Ion	CALCIUM ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:241 , LEU A:243 , VAL A:246 , DC C:26	BINDING SITE FOR RESIDUE CA C 302

(no "SS Bond" information available for 2NOZ)

(no "Cis Peptide Bond" information available for 2NOZ)

Asymmetric/Biological Unit (10, 10)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_024831	G	12	E	OGG1_HUMAN	Polymorphism	772520254	A	G	12	E
02	UniProt	VAR_009519	R	46	Q	OGG1_HUMAN	Polymorphism	104893751	A	R	46	Q
03	UniProt	VAR_024832	A	85	S	OGG1_HUMAN	Polymorphism	17050550	A	A	85	S
04	UniProt	VAR_024833	R	131	Q	OGG1_HUMAN	Polymorphism	747638147	A	R	131	Q
05	UniProt	VAR_009520	R	154	H	OGG1_HUMAN	Polymorphism	56053615	A	R	154	H
06	UniProt	VAR_014487	R	229	Q	OGG1_HUMAN	Polymorphism	1805373	A	R	229	Q
07	UniProt	VAR_024834	S	232	T	OGG1_HUMAN	Unclassified	---	A	S	232	T
08	UniProt	VAR_018890	A	288	V	OGG1_HUMAN	Polymorphism	3219012	A	A	288	V
09	UniProt	VAR_014488	S	320	T	OGG1_HUMAN	Polymorphism	1801128	A	S	320	T
10	UniProt	VAR_018891	D	322	N	OGG1_HUMAN	Polymorphism	3219014	A	D	322	N

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 2NOZ)

Asymmetric/Biological Unit (7, 7)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000344629	1a	ENSE00002157661	chr3:9791628-9792107	480	OGG1_HUMAN	1-46	46	1	A:9-46	38
1.2b	ENST00000344629	2b	ENSE00001669842	chr3:9792629-9792876	248	OGG1_HUMAN	46-129	84	1	A:46-129 (gaps)	84
1.3a	ENST00000344629	3a	ENSE00001644854	chr3:9793454-9793633	180	OGG1_HUMAN	129-189	61	1	A:129-189	61
1.4	ENST00000344629	4	ENSE00001165146	chr3:9796388-9796569	182	OGG1_HUMAN	189-249	61	1	A:189-249	61
1.5	ENST00000344629	5	ENSE00001661907	chr3:9798155-9798305	151	OGG1_HUMAN	250-300	51	1	A:250-300 (gaps)	51
1.6a	ENST00000344629	6a	ENSE00001764469	chr3:9798451-9798500	50	OGG1_HUMAN	300-316	17	1	A:300-316	17
1.6j	ENST00000344629	6j	ENSE00001651617	chr3:9798745-9799197	453	OGG1_HUMAN	317-345	29	1	A:317-323	7

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:310
 aligned with OGG1_HUMAN | O15527 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:315
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318     
           OGG1_HUMAN     9 RRMGHRTLASTPALWASIPCPRSELRLDLVLPSGQSFRWREQSPAHWSGVLADQVWTLTQTEEQLHCTVYRGDKSQASRPTPDELEAVRKYFQLDVTLAQLYHHWGSVDSHFQEVAQKFQGVRLLRQDPIECLFSFICSSNNNIARITGMVERLCQAFGPRLIQLDDVTYHGFPSLQALAGPEVEAHLRKLGLGYRARYVSASARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGTKVADCICLMALDKPQAVPVDVHMWHIAQRDYSWHPTTSQAKGPSPQTNKELGNFFRSLWGPYAGWAQAVLFSADL 323
               SCOP domains d2noza2 A:9-135 8-oxoguanine glycosylase                                                                                       d2noza1 A:136-323 8-oxoguanine glycosylase                                                                                                                                                   SCOP domains
               CATH domains 2nozA01 A:9-100  [code=3.30.310.40, no name defined]                                        ---2nozA02              -----------2nozA03 A:136-261 Hypothetical protein; domain 2                                                                              ---2nozA02 A:104-124,A:2  65-323                               CATH domains
               Pfam domains ----------------OGG_N-2nozA02 A:25-141                                                                                               HhH-GPD-2nozA01 A:142-301                                                                                                                                       ---------------------- Pfam domains
         Sec.struct. author ..........hhhhheeee......hhhhhh........eeee..eeeeee..eeeeeee...eeeeeee.---......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh....hhhhhhhhhhhhhhhhh.eeeee..eeee...hhhhhh..hhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhh...hhhhhhhhhh.....hhhhhhhhhhhh.........hhhhhhhhhhhhh.....--....hhhhhhhhhhhhhhhhh.hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---E---------------------------------Q--------------------------------------S---------------------------------------------Q----------------------H--------------------------------------------------------------------------Q--T-------------------------------------------------------V-------------------------------T-N- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:9-46 UniProt: 1-46  ----------------------------------------------------------------------------------Exon 1.3a  PDB: A:129-189 UniProt: 129-189                   ------------------------------------------------------------Exon 1.5  PDB: A:250-300 (gaps) UniProt: 250-300   ----------------1.6j    Transcript 1 (1)
           Transcript 1 (2) -------------------------------------Exon 1.2b  PDB: A:46-129 (gaps) UniProt: 46-129                                     -----------------------------------------------------------Exon 1.4  PDB: A:189-249 UniProt: 189-249                    --------------------------------------------------Exon 1.6a        ------- Transcript 1 (2)
                 2noz A   9 SEFGHRTLASTPALWASIPCPRSELRLDLVLPSGQSFRWREQSPAHWSGVLADQVWTLTQTEEQLHCTVYR---SQASRPTPDELEAVRKYFQLDVTLAQLYHHWGSVDSHFQEVAQKFQGVRLLRQDPIECLFSFICSSNNNIARITGMVERLCQAFGPRLIQLDDVTYHGFPSLQALAGPEVEAHLRKLGLGYRARYVSASARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGTKVADCICLMALDKPQAVPVDVHMWHIAQRDYSWHPTT--AKGPCPQTNKELGNFFRSLWGPYAGWAFAVLFSADL 323
                                    18        28        38        48        58        68        78|   |   88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278      |288       298       308       318     
                                                                                                 79  83                                                                                                                                                                                                       285  |                                   
                                                                                                                                                                                                                                                                                                                 288

Chain B from PDB  Type:DNA  Length:11
                                           
                 2noz B   3 TAGACCTGGAC  13
                                    12

Chain C from PDB  Type:DNA  Length:12
                                            
                 2noz C  17 CGTCCAgGTCTA  28
                                  | 26  
                                 23-8OG

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: TATA-Binding Protein (118)

Homologous Superfamily: [code=3.30.310.40, no name defined] (24)

[unclassified] (23)

2nozA01

A:9-100

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Endonuclease Iii, domain 2 (65)

Homologous Superfamily: Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) (65)

[unclassified] (30)

2nozA02

A:104-124,A:265-323

Topology: Endonuclease III; domain 1 (74)

Homologous Superfamily: Hypothetical protein; domain 2 (73)

[unclassified] (31)

2nozA03

A:136-261

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HHH (112)

Family: HhH-GPD (47)

Homo sapiens (Human) (22)

HhH-GPD-2nozA01

A:142-301

Clan: TBP-like (48)

Family: OGG_N (21)

Homo sapiens (Human) (21)

OGG_N-2nozA02

A:25-141

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (OGG1_HUMAN | O15527)

molecular function
	GO:0034039	8-oxo-7,8-dihydroguanine DNA N-glycosylase activity	Catalysis of the removal of 8-oxo-7,8-dihydroguanine bases by cleaving the N-C1' glycosidic bond between the oxidized purine and the deoxyribose sugar.
	GO:0019104	DNA N-glycosylase activity	Catalysis of the removal of damaged bases by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apurinic/apyrimidinic (AP) site.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003906	DNA-(apurinic or apyrimidinic site) endonuclease activity	Catalysis of the cleavage of the C-O-P bond in the AP site created when DNA glycosylase removes a damaged base, involved in the DNA base excision repair pathway (BER).
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0003684	damaged DNA binding	Interacting selectively and non-covalently with damaged DNA.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016798	hydrolase activity, acting on glycosyl bonds	Catalysis of the hydrolysis of any glycosyl bond.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0008017	microtubule binding	Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
	GO:0032357	oxidized purine DNA binding	Interacting selectively and non-covalently with oxidized purine residues in DNA.
	GO:0008534	oxidized purine nucleobase lesion DNA N-glycosylase activity	Catalysis of the removal of oxidized purine bases by cleaving the N-C1' glycosidic bond between the oxidized purine and the deoxyribose sugar. The reaction involves the formation of a covalent enzyme-substrate intermediate. Release of the enzyme and free base by a beta-elimination or a beta, gamma-elimination mechanism results in the cleavage of the DNA backbone 3' of the apurinic (AP) site.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0006281	DNA repair	The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
	GO:0002526	acute inflammatory response	Inflammation which comprises a rapid, short-lived, relatively uniform response to acute injury or antigenic challenge and is characterized by accumulations of fluid, plasma proteins, and granulocytic leukocytes. An acute inflammatory response occurs within a matter of minutes or hours, and either resolves within a few days or becomes a chronic inflammatory response.
	GO:0007568	aging	A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
	GO:0006284	base-excision repair	In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0071276	cellular response to cadmium ion	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cadmium (Cd) ion stimulus.
	GO:0045007	depurination	The disruption of the bond between the sugar in the backbone and the A or G base, causing the base to be removed and leaving a depurinated sugar.
	GO:0045008	depyrimidination	The disruption of the bond between the sugar in the backbone and the C or T base, causing the base to be removed and leaving a depyrimidinated sugar.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:1901291	negative regulation of double-strand break repair via single-strand annealing	Any process that stops, prevents or reduces the frequency, rate or extent of double-strand break repair via single-strand annealing.
	GO:0006289	nucleotide-excision repair	A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
	GO:0033683	nucleotide-excision repair, DNA incision	A process that results in the endonucleolytic cleavage of the damaged strand of DNA. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound.
	GO:0033158	regulation of protein import into nucleus, translocation	Any process that modulates the vectorial transfer of a protein from the cytoplasm into the nucleus, across the nuclear membrane.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0042493	response to drug	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0032355	response to estradiol	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
	GO:0045471	response to ethanol	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ethanol stimulus.
	GO:0051593	response to folic acid	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a folic acid stimulus.
	GO:0009416	response to light stimulus	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light.
	GO:0006979	response to oxidative stress	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
	GO:0009314	response to radiation	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation.
cellular component
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0016363	nuclear matrix	The dense fibrillar network lying on the inner side of the nuclear membrane.
	GO:0016607	nuclear speck	A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric/Biological Unit
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	2noz
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1ebm	HOGG1 COMPLEXED WITH OXOG CONTAINING DNA
1yqk	HOGG1 CROSSLINKED TO DNA SAMPLING AN UNDAMAGED G
1yqr	CATALYTICALLY INACTIVE HOGG1 CROSSLINKED TO OXOG CONTAINING DNA
2nob
2noe
2nof
2noh
2noi
2nol

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (10, 10)

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Exons (7, 7)

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SCOP Domains (2, 2)

CATH Domains (3, 3)

Pfam Domains (2, 2)

Gene Ontology (41, 41)

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